Step 1) The night before: Combine pinto and chick peas in a large bowl; add water to cover beans by 1 inch. Cover bowl. Combine black beans in a separate bowl; add water to cover beans by 1 inch. Cover bowl. Let both bowls of beans stand overnight at room temperature.
Step 2) In the morning, heat oil in a medium nonstick skillet. Add onion and garlic and cook just until onion is just starting to brown; add chili powder and cook for 1 to 2 minutes. Set aside.
Step 3) Drain beans.
Step 4) Combine beans, onion mixture, rice, broth, boiling water, cocoa powder, chipotle chile powder, cinnamon and agave nectar in a greased 4 to 5-quart slow cooker. Stir to combine.
Step 5) Slow cook on LOW for 8 to 10 hours, until beans are tender. Stir in tomatoes.
Step 6) Serve bowls of chili garnished with yogurt and pepitas.
Recipe Note: In place of an overnight soak, you can do a Quick Soak. To do, bring pinto and garbanzo beans and 3 cups water to a boil in a medium saucepan. Cover and remove from heat. Bring black beans and 2 cups water to a boil in a small saucepan. Cover and remove from heat. Let beans stand for 1 hour; drain, rinse and proceed with recipe. Can cook all three beans together but the black beans will turn the chickpeas purple!